 Alexander Ruthenburg
| Title | Associate Professor |
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| Institution | University of Chicago |
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| Department | Mol Gen/Cell Bio |
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| Address | Chicago IL 60637
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| Email |  |
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| vCard | Download vCard |
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 Overview The unifying theme of my lab is the elucidation of molecular mechanisms underlying management chromatin, the physiological form of the genome. In particular, we are interested in how post translational modifications to histones, newly appreciated DNA modifications and noncoding RNA can control chromatin structure. Our research spans several traditional disciplines, ranging from discovery biochemistry and genome-scale measurements to mechanistic characterization with biophysical methods coupled with X-Ray structure to address fundamental questions in chromatin biology. We have pioneered new technologies to make quantitative local measurements of chromatin components. Projects ideally will transition from discovery biology to detailed molecular and structural investigation.
Biography | Rockefeller University , New York, NY | Postdoctoral Fellow | 8/2010 | Chromatin biochemsitry and epigenetics | | Harvard University , Cambridge, MA | Ph.D. | 9/2005 | Chemical and Structural biology | | Carleton College, Northfield, MN | B.A. | 6/1999 | Chemistry |
| 2011 | Kavli Fellow, National Academy of Sciences | | 2013 - 2017 | New Scholar in Aging, Ellison Medical Foundation | | 2010 - 2015 | Neubauer Family Foundation Assistant Professor, University of Chicago | | 2010 - 2012 | Junior Investigator, Chicago Biomedical Consortium | | 2007 - 2010 | Irvington Institute Research Fellowship, Cancer Research Institute | | 2000 - 2004 | National Science Foundation Graduate Research Fellow , Harvard University |
ORNG Applications Research AG-NS-1118-13 (Ruthenburg)Aug 1, 2013 - Aug 1, 2017 Ellison Medical Foundation
Discovery of New Epigenetic Pathways involved in stem sell maintenance
Role: Principal Investigator |
| R21HG007426 (RUTHENBURG, ALEXANDER JACKSON)Aug 22, 2013 - May 31, 2015 NIH
Calibrated ChIP-seq: determining local histone modification density genome-wide
Role: Principal Investigator |
| R44-HG008907 (Zu-Wen Sun)Dec 15, 2015 - Nov 30, 2017 NIH
Internally calibrated chromatin immunoprecipitation using barcoded nucleosomes
Role Description: This is a phase II SBIR centered on commercializing the ICeChIP technology developed in my lab. Two products are now on the market, offered by Epicypher, Inc: SNAP-ChIP and CAP-ChIP.
Role: Co-investigator |
| R01GM115945 (RUTHENBURG, ALEXANDER JACKSON)Apr 6, 2016 - Mar 31, 2021 NIH
Quantitatively probing intra-nucleosomal chromatin variation and function
Role: Principal Investigator |
| RSG-16-248-01-DMC (Ruthenburg)Jan 1, 2017 - Dec 31, 2020 American Cancer Society
Biochemical discovery of new epigenetic pathways linked to leukemia
Role: Principal Invesitgator |
| 17CSA33610126 (Moskowitz & Ruthenburg)Jul 1, 2017 American Heart Association
Enhancer transcription as marker and modulator of cardiac regulatory networks
Role Description: Collaborative Sciences Award
Role: Co-PI |
Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications.
Faculty can login to make corrections and additions.
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Oikawa M, Simeone A, Hormanseder E, Teperek M, Gaggioli V, O'Doherty A, Falk E, Sporniak M, D'Santos C, Franklin VNR, Kishore K, Bradshaw CR, Keane D, Freour T, David L, Grzybowski AT, Ruthenburg AJ, Gurdon J, Jullien J. Epigenetic homogeneity in histone methylation underlies sperm programming for embryonic transcription. Nat Commun. 2020 Jul 13; 11(1):3491. PMID: 32661239.
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Sun X, Wang Z, Hall JM, Perez-Cervantes C, Ruthenburg AJ, Moskowitz IP, Gribskov M, Yang XH. Chromatin-enriched RNAs mark active and repressive cis-regulation: An analysis of nuclear RNA-seq. PLoS Comput Biol. 2020 02; 16(2):e1007119. PMID: 32040509.
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Grzybowski AT, Shah RN, Richter WF, Ruthenburg AJ. Native internally calibrated chromatin immunoprecipitation for quantitative studies of histone post-translational modifications. Nat Protoc. 2019 12; 14(12):3275-3302. PMID: 31723301.
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Bennett RL, Bele A, Small EC, Will CM, Nabet B, Oyer JA, Huang X, Ghosh RP, Grzybowski AT, Yu T, Zhang Q, Riva A, Lele TP, Schatz GC, Kelleher NL, Ruthenburg AJ, Liphardt J, Licht JD. A Mutation in Histone H2B Represents a New Class of Oncogenic Driver. Cancer Discov. 2019 10; 9(10):1438-1451. PMID: 31337617.
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Shah RN, Grzybowski AT, Cornett EM, Johnstone AL, Dickson BM, Boone BA, Cheek MA, Cowles MW, Maryanski D, Meiners MJ, Tiedemann RL, Vaughan RM, Arora N, Sun ZW, Rothbart SB, Keogh MC, Ruthenburg AJ. Examining the Roles of H3K4 Methylation States with Systematically Characterized Antibodies. Mol Cell. 2018 10 04; 72(1):162-177.e7. PMID: 30244833.
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Karki S, Kennedy DE, Mclean K, Grzybowski AT, Maienschein-Cline M, Banerjee S, Xu H, Davis E, Mandal M, Labno C, Powers SE, Le Beau MM, Dinner AR, Singh H, Ruthenburg AJ, Clark MR. Regulated Capture of V? Gene Topologically Associating Domains by Transcription Factories. Cell Rep. 2018 08 28; 24(9):2443-2456. PMID: 30157436.
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Maganti HB, Jrade H, Cafariello C, Manias Rothberg JL, Porter CJ, Yockell-Lelièvre J, Battaion HL, Khan ST, Howard JP, Li Y, Grzybowski AT, Sabri E, Ruthenburg AJ, Dilworth FJ, Perkins TJ, Sabloff M, Ito CY, Stanford WL. Targeting the MTF2-MDM2 Axis Sensitizes Refractory Acute Myeloid Leukemia to Chemotherapy. Cancer Discov. 2018 11; 8(11):1376-1389. PMID: 30115703.
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Gupta A, Xu J, Lee S, Tsai ST, Zhou B, Kurosawa K, Werner MS, Koide A, Ruthenburg AJ, Dou Y, Koide S. Facile target validation in an animal model with intracellularly expressed monobodies. Nat Chem Biol. 2018 09; 14(9):895-900. PMID: 30013062.
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Yang XH, Nadadur RD, Hilvering CR, Bianchi V, Werner M, Mazurek SR, Gadek M, Shen KM, Goldman JA, Tyan L, Bekeny J, Hall JM, Lee N, Perez-Cervantes C, Burnicka-Turek O, Poss KD, Weber CR, de Laat W, Ruthenburg AJ, Moskowitz IP. Transcription-factor-dependent enhancer transcription defines a gene regulatory network for cardiac rhythm. Elife. 2017 12 27; 6. PMID: 29280435.
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Chen Z, Notti RQ, Ueberheide B, Ruthenburg AJ. Quantitative and Structural Assessment of Histone Methyllysine Analogue Engagement by Cognate Binding Proteins Reveals Affinity Decrements Relative to Those of Native Counterparts. Biochemistry. 2018 01 23; 57(3):300-304. PMID: 29111671.
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Werner MS, Sullivan MA, Shah RN, Nadadur RD, Grzybowski AT, Galat V, Moskowitz IP, Ruthenburg AJ. Chromatin-enriched lncRNAs can act as cell-type specific activators of proximal gene transcription. Nat Struct Mol Biol. 2017 Jul; 24(7):596-603. PMID: 28628087.
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Hattori T, Lai D, Dementieva IS, Montaño SP, Kurosawa K, Zheng Y, Akin LR, Swist-Rosowska KM, Grzybowski AT, Koide A, Krajewski K, Strahl BD, Kelleher NL, Ruthenburg AJ, Koide S. Antigen clasping by two antigen-binding sites of an exceptionally specific antibody for histone methylation. Proc Natl Acad Sci U S A. 2016 Feb 23; 113(8):2092-7. PMID: 26862167.
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Werner MS, Ruthenburg AJ. Nuclear Fractionation Reveals Thousands of Chromatin-Tethered Noncoding RNAs Adjacent to Active Genes. Cell Rep. 2015 Aug 18; 12(7):1089-98. PMID: 26257179.
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Rothbart SB, Dickson BM, Raab JR, Grzybowski AT, Krajewski K, Guo AH, Shanle EK, Josefowicz SZ, Fuchs SM, Allis CD, Magnuson TR, Ruthenburg AJ, Strahl BD. An Interactive Database for the Assessment of Histone Antibody Specificity. Mol Cell. 2015 Aug 06; 59(3):502-11. PMID: 26212453.
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Grzybowski AT, Chen Z, Ruthenburg AJ. Calibrating ChIP-Seq with Nucleosomal Internal Standards to Measure Histone Modification Density Genome Wide. Mol Cell. 2015 Jun 04; 58(5):886-99. PMID: 26004229.
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Chen Z, Grzybowski AT, Ruthenburg AJ. Traceless semisynthesis of a set of histone 3 species bearing specific lysine methylation marks. Chembiochem. 2014 Sep 22; 15(14):2071-5. PMID: 25155436.
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Hattori T, Taft JM, Swist KM, Luo H, Witt H, Slattery M, Koide A, Ruthenburg AJ, Krajewski K, Strahl BD, White KP, Farnham PJ, Zhao Y, Koide S. Recombinant antibodies to histone post-translational modifications. Nat Methods. 2013 Oct; 10(10):992-5. PMID: 23955773.
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Mohrig JR, Beyer BG, Fleischhacker AS, Ruthenburg AJ, John SG, Snyder DA, Nyffeler PT, Noll RJ, Penner ND, Phillips LA, Hurley HL, Jacobs JS, Treitel C, James TL, Montgomery MP. Does activation of the anti proton, rather than concertedness, determine the stereochemistry of base-catalyzed 1,2-elimination reactions? Anti stereospecificity in E1cB eliminations of ß-3-trifluoromethylphenoxy esters, thioesters, and ketones. J Org Chem. 2012 Mar 16; 77(6):2819-28. PMID: 22321002.
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Malecek K, Ruthenburg A. Validation of histone-binding partners by peptide pull-downs and isothermal titration calorimetry. Methods Enzymol. 2012; 512:187-220. PMID: 22910208.
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Werner M, Ruthenburg AJ. The United States of histone ubiquitylation and methylation. Mol Cell. 2011 Jul 08; 43(1):5-7. PMID: 21726805.
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Ruthenburg AJ, Li H, Milne TA, Dewell S, McGinty RK, Yuen M, Ueberheide B, Dou Y, Muir TW, Patel DJ, Allis CD. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell. 2011 May 27; 145(5):692-706. PMID: 21596426.
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Milne TA, Kim J, Wang GG, Stadler SC, Basrur V, Whitcomb SJ, Wang Z, Ruthenburg AJ, Elenitoba-Johnson KS, Roeder RG, Allis CD. Multiple interactions recruit MLL1 and MLL1 fusion proteins to the HOXA9 locus in leukemogenesis. Mol Cell. 2010 Jun 25; 38(6):853-63. PMID: 20541448.
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Ruthenburg AJ, Li H, Patel DJ, Allis CD. Multivalent engagement of chromatin modifications by linked binding modules. Nat Rev Mol Cell Biol. 2007 Dec; 8(12):983-94. PMID: 18037899.
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Taverna SD, Li H, Ruthenburg AJ, Allis CD, Patel DJ. How chromatin-binding modules interpret histone modifications: lessons from professional pocket pickers. Nat Struct Mol Biol. 2007 Nov; 14(11):1025-1040. PMID: 17984965.
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Ruthenburg AJ, Allis CD, Wysocka J. Methylation of lysine 4 on histone H3: intricacy of writing and reading a single epigenetic mark. Mol Cell. 2007 Jan 12; 25(1):15-30. PMID: 17218268.
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Dou Y, Milne TA, Ruthenburg AJ, Lee S, Lee JW, Verdine GL, Allis CD, Roeder RG. Regulation of MLL1 H3K4 methyltransferase activity by its core components. Nat Struct Mol Biol. 2006 Aug; 13(8):713-9. PMID: 16878130.
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Ruthenburg AJ, Wang W, Graybosch DM, Li H, Allis CD, Patel DJ, Verdine GL. Histone H3 recognition and presentation by the WDR5 module of the MLL1 complex. Nat Struct Mol Biol. 2006 Aug; 13(8):704-12. PMID: 16829959.
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Losey HC, Ruthenburg AJ, Verdine GL. Crystal structure of Staphylococcus aureus tRNA adenosine deaminase TadA in complex with RNA. Nat Struct Mol Biol. 2006 Feb; 13(2):153-9. PMID: 16415880.
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Wei H, Ruthenburg AJ, Bechis SK, Verdine GL. Nucleotide-dependent domain movement in the ATPase domain of a human type IIA DNA topoisomerase. J Biol Chem. 2005 Nov 04; 280(44):37041-7. PMID: 16100112.
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Ruthenburg AJ, Graybosch DM, Huetsch JC, Verdine GL. A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias. J Biol Chem. 2005 Jul 15; 280(28):26177-84. PMID: 15897198.
This graph shows the total number of publications by year, by first, middle/unknown, or last author.
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| Year | Publications |
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| 2005 | 2 | | 2006 | 3 | | 2007 | 3 | | 2010 | 1 | | 2011 | 2 | | 2012 | 2 | | 2013 | 1 | | 2014 | 1 | | 2015 | 3 | | 2016 | 1 | | 2017 | 3 | | 2018 | 4 | | 2019 | 2 | | 2020 | 2 |
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